6HCU

Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum bound to a difluoro cyclohexyl chromone ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Lysyl-tRNA synthetase as a drug target in malaria and cryptosporidiosis.

Baragana, B.Forte, B.Choi, R.Nakazawa Hewitt, S.Bueren-Calabuig, J.A.Pisco, J.P.Peet, C.Dranow, D.M.Robinson, D.A.Jansen, C.Norcross, N.R.Vinayak, S.Anderson, M.Brooks, C.F.Cooper, C.A.Damerow, S.Delves, M.Dowers, K.Duffy, J.Edwards, T.E.Hallyburton, I.Horst, B.G.Hulverson, M.A.Ferguson, L.Jimenez-Diaz, M.B.Jumani, R.S.Lorimer, D.D.Love, M.S.Maher, S.Matthews, H.McNamara, C.W.Miller, P.O'Neill, S.Ojo, K.K.Osuna-Cabello, M.Pinto, E.Post, J.Riley, J.Rottmann, M.Sanz, L.M.Scullion, P.Sharma, A.Shepherd, S.M.Shishikura, Y.Simeons, F.R.C.Stebbins, E.E.Stojanovski, L.Straschil, U.Tamaki, F.K.Tamjar, J.Torrie, L.S.Vantaux, A.Witkowski, B.Wittlin, S.Yogavel, M.Zuccotto, F.Angulo-Barturen, I.Sinden, R.Baum, J.Gamo, F.J.Maser, P.Kyle, D.E.Winzeler, E.A.Myler, P.J.Wyatt, P.G.Floyd, D.Matthews, D.Sharma, A.Striepen, B.Huston, C.D.Gray, D.W.Fairlamb, A.H.Pisliakov, A.V.Walpole, C.Read, K.D.Van Voorhis, W.C.Gilbert, I.H.

(2019) Proc Natl Acad Sci U S A 116: 7015-7020

  • DOI: https://doi.org/10.1073/pnas.1814685116
  • Primary Citation of Related Structures:  
    5ELN, 5ELO, 6AGT, 6HCU, 6HCV, 6HCW

  • PubMed Abstract: 

    Malaria and cryptosporidiosis, caused by apicomplexan parasites, remain major drivers of global child mortality. New drugs for the treatment of malaria and cryptosporidiosis, in particular, are of high priority; however, there are few chemically validated targets. The natural product cladosporin is active against blood- and liver-stage Plasmodium falciparum and Cryptosporidium parvum in cell-culture studies. Target deconvolution in P. falciparum has shown that cladosporin inhibits lysyl-tRNA synthetase ( Pf KRS1). Here, we report the identification of a series of selective inhibitors of apicomplexan KRSs. Following a biochemical screen, a small-molecule hit was identified and then optimized by using a structure-based approach, supported by structures of both Pf KRS1 and C. parvum KRS ( Cp KRS). In vivo proof of concept was established in an SCID mouse model of malaria, after oral administration (ED 90 = 1.5 mg/kg, once a day for 4 d). Furthermore, we successfully identified an opportunity for pathogen hopping based on the structural homology between Pf KRS1 and Cp KRS. This series of compounds inhibit Cp KRS and C. parvum and Cryptosporidium hominis in culture, and our lead compound shows oral efficacy in two cryptosporidiosis mouse models. X-ray crystallography and molecular dynamics simulations have provided a model to rationalize the selectivity of our compounds for Pf KRS1 and Cp KRS vs. (human) Hs KRS. Our work validates apicomplexan KRSs as promising targets for the development of drugs for malaria and cryptosporidiosis.


  • Organizational Affiliation

    Medicines for Malaria Venture, 1215 Geneva 15, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysine--tRNA ligase
A, B
507Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1350100
EC: 6.1.1.6
UniProt
Find proteins for Q8IDJ8 (Plasmodium falciparum (isolate 3D7))
Explore Q8IDJ8 
Go to UniProtKB:  Q8IDJ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IDJ8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FYB
Query on FYB

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
~{N}-[[4,4-bis(fluoranyl)-1-oxidanyl-cyclohexyl]methyl]-6-fluoranyl-4-oxidanylidene-chromene-2-carboxamide
C17 H16 F3 N O4
PJBRCGHQNUWERQ-UHFFFAOYSA-N
HIS
Query on HIS

Download Ideal Coordinates CCD File 
F [auth A]HISTIDINE
C6 H10 N3 O2
HNDVDQJCIGZPNO-YFKPBYRVSA-O
LYS
Query on LYS

Download Ideal Coordinates CCD File 
D [auth A]LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
TRS
Query on TRS

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
J [auth B],
K [auth B]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG
Query on PEG

Download Ideal Coordinates CCD File 
E [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
FYB Binding MOAD:  6HCU IC50: 15 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.137α = 90
b = 95.344β = 90
c = 166.517γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
autoPROCdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesOPP1032548

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description